# Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r4.ebuild,v 1.2 2010/06/24 18:04:40 jlec Exp $ EAPI="3" PYTHON_DEPEND="2" inherit autotools eutils flag-o-matic fortran gnuconfig python toolchain-funcs FORTRAN="g77 gfortran ifc" MY_P="${PN/-apps}-${PV}" SRC="ftp://ftp.ccp4.ac.uk/ccp4" #UPDATE="04_03_09" #PATCHDATE="090511" PATCH_TOT="0" # Here's a little scriptlet to generate this list from the provided # index.patches file # # i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; # echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < # index.patches #PATCH1=( src/topp_ #topp.f-r1.16.2.5-r1.16.2.6.diff ) #PATCH2=( . #configure-r1.372.2.18-r1.372.2.19.diff ) DESCRIPTION="Protein X-ray crystallography toolkit" HOMEPAGE="http://www.ccp4.ac.uk/" RESTRICT="mirror" SRC_URI=" ${SRC}/${PV}/${MY_P}-core-src.tar.gz http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" # patch tarball from upstream [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" # patches created by us [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" for i in $(seq $PATCH_TOT); do NAME="PATCH${i}[1]" SRC_URI="${SRC_URI} ${SRC}/${PV}/patches/${!NAME}" done LICENSE="ccp4" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="examples X" X11DEPS=" x11-libs/libX11 x11-libs/libXaw x11-libs/libXt x11-libs/libxdl_view" TKDEPS=" >=dev-lang/tk-8.3 >=dev-tcltk/blt-2.4 dev-tcltk/iwidgets dev-tcltk/itcl dev-tcltk/itk >=dev-tcltk/tdom-0.8 dev-tcltk/tkimg dev-tcltk/tktreectrl" SCILIBS=" ~sci-libs/ccp4-libs-${PV} >=sci-libs/ccp4-libs-${PV}-r2 sci-libs/clipper =sci-libs/fftw-2* sci-libs/mmdb virtual/blas virtual/lapack" SCIAPPS=" sci-chemistry/pdb-extract sci-chemistry/pymol sci-chemistry/rasmol >=sci-chemistry/oasis-4.0-r1" RDEPEND=" ${TKDEPS} ${SCILIBS} app-shells/tcsh dev-python/pyxml dev-libs/libxml2 dev-libs/libjwc_c dev-libs/libjwc_f dev-libs/boehm-gc !app-office/sc !<sci-chemistry/ccp4-6.1.2 X? ( ${X11DEPS} )" DEPEND="${RDEPEND} =sys-devel/automake-1.6* X? ( x11-misc/imake x11-proto/inputproto x11-proto/xextproto )" PDEPEND="${SCIAPPS}" S="${WORKDIR}/${MY_P}" pkg_setup() { python_set_active_version 2 fortran_pkg_setup } src_prepare() { einfo "Applying upstream patches ..." for patch in $(seq $PATCH_TOT); do base="PATCH${patch}" dir=$(eval echo \${${base}[0]}) p=$(eval echo \${${base}[1]}) pushd "${dir}" >& /dev/null ccp_patch ${DISTDIR}/"${p}" popd >& /dev/null done einfo "Done." echo [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch einfo "Applying Gentoo patches ..." # it tries to create libdir, bindir etc on live system in configure ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch # We already have sci-chemistry/rasmol # Also remember to create the bindir. ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch # libraries come from sci-libs/ccp4-libs ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch # coreutils installs a binary called truncate # ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch # mv ./doc/truncate.doc ./doc/ftruncate.doc || die # mv ./html/truncate.html ./html/ftruncate.html || die # conflicts with media-libs/raptor # ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch # mv ./doc/rapper.doc ./doc/rappermc.doc || die # mv ./html/rapper.html ./html/rappermc.html || die # We have seperate ebuilds for those for bin in molref xia scala imosflm balbes; do ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch done # don't configure what is not build ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch # Set python paths correctly ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch # Set python paths correctly ccp_patch "${FILESDIR}"/${PV}-pisa.patch # Set python paths correctly ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch # Update things for oasis 4 usage epatch "${WORKDIR}"/${PV}-oasis4.0.patch sed 's: oasis : :g' -i src/Makefile.in || die einfo "Done." # done applying Gentoo patches echo # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. pushd src/rapper 2>/dev/null sed -i \ -e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \ configure.ac sed -i \ -e '/^SUBDIRS/s:libxml2 gc7.0::g' \ Makefile.am sed -i \ -e '/^rapper_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \ LOOP/Makefile.am sed -i \ -e "/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I${EPREFIX}/usr/include/gc -I${EPREFIX}/usr/include/libxml2:g" \ LOOP/Makefile.am eautoreconf popd 2>/dev/null gnuconfig_update python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py } src_configure() { # Build system is broken if we set LDFLAGS unset LDFLAGS # These are broken with ./src/procheck/ps.f filter-flags "-floop-*" # GENTOO_OSNAME can be one of: # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd # linux_compaq_compilers linux_intel_compilers generic Darwin # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers if [[ "${FORTRANC}" = "ifc" ]]; then if use ia64; then GENTOO_OSNAME="ia64_linux_intel" else # Should be valid for x86, maybe amd64 GENTOO_OSNAME="linux_intel_compilers" fi else # Should be valid for x86 and amd64, at least GENTOO_OSNAME="linux" fi # Sets up env ln -s \ ccp4.setup-bash \ "${S}"/include/ccp4.setup # We agree to the license by emerging this, set in LICENSE sed -i \ -e "s~^\(^agreed=\).*~\1yes~g" \ "${S}"/configure # Fix up variables -- need to reset CCP4_MASTER at install-time sed -i \ -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ -e "s~^\(export CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ "${S}"/include/ccp4.setup* # Set up variables for build source "${S}"/include/ccp4.setup-sh export CC=$(tc-getCC) export CXX=$(tc-getCXX) export COPTIM=${CFLAGS} export CXXOPTIM=${CXXFLAGS} # Default to -O2 if FFLAGS is unset export FC=${FORTRANC} export FOPTIM=${FFLAGS:- -O2} export BINSORT_SCR="${T}" export CCP4_MASTER="${WORKDIR}" export CCP4I_TCLTK="${EPREFIX}/usr/bin" # Can't use econf, configure rejects unknown options like --prefix ./configure \ $(use_enable X x) \ --with-shared-libs \ --with-fftw="${EPREFIX}"/usr \ --with-warnings \ --disable-pdb_extract \ --disable-cctbx \ --disable-phaser \ --disable-diffractionImg \ --disable-clipper \ --disable-mosflm \ --disable-mrbump \ --tmpdir="${TMPDIR}" \ ${GENTOO_OSNAME} || die "econf failed" # We do this manually, since disabling the clipper libraries also # disables the clipper programs pushd src/clipper_progs 2>/dev/null econf \ --prefix="${S}" \ --bindir="${ED}"/usr/libexec/ccp4/bin \ --with-ccp4="${S}" \ --with-clipper="${EPREFIX}"/usr \ --with-fftw="${EPREFIX}"/usr \ --with-mmdb="${EPREFIX}"/usr \ CXX=$(tc-getCXX) \ || die popd 2>/dev/null } src_compile() { # fsplit is required for the programs pushd lib/src 2>/dev/null emake fsplit -j1 || die popd 2>/dev/null # We do this manually, since disabling the clipper libraries also # disables the clipper programs pushd src/clipper_progs 2>/dev/null emake || die popd 2>/dev/null emake -j1 || die "emake failed" } src_install() { # Set up variables for build source "${S}"/include/ccp4.setup-sh # make install || die "install failed" # if we don't make this, a ton of programs fail to install mkdir "${S}"/bin || die # We do this manually, since disabling the clipper libraries also # disables the clipper programs pushd "${S}"/src/clipper_progs 2>/dev/null emake install || die popd 2>/dev/null einstall || die "install failed" # Fix env # -e "s~^\(.*setenv PYTHONPATH .*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \ # -e "s~^\(.*export PYTHONPATH.*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \ sed -i \ -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \ -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \ -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ -e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \ -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \ -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \ -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ -e "s~^\(.*setenv CLIB .*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "s~^\(export CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \ -e "s~^\(export CCP4.*\$CCP4_MASTER\).*~\1~g" \ -e "s~^\(export CCP4I_TOP\).*~\1=\$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ -e "s~^\(export DBCCP4I_TOP\).*~\1=\$CCP4/share/ccp4/dbccp4i~g" \ -e "s~^\(.*export CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \ -e "s~^\(.*export CLIBD.*\$CCP4\).*~\1/share/ccp4/data~g" \ -e "s~^\(.*export CLIBD_MON.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ -e "s~^\(.*export MOLREPLIB.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \ -e "s~^\(.*export CLIB=.*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ -e "/IMOSFLM_VERSION/d" \ "${S}"/include/ccp4.setup* || die # -e "s~\$CCP4/share/XIAROOT/setup.sh~\$CCP4/share/ccp4/XIAROOT/setup.sh~g" \ # Don't check for updates on every sourcing of /etc/profile sed -i \ -e "s:\(eval python.*\):#\1:g" "${S}"/include/ccp4.setup* || die # Collision with sci-chemistry/mrbump rm -f "${S}"/bin/{mrbump,pydbviewer} || die # Bins exeinto /usr/libexec/ccp4/bin/ doexe "${S}"/bin/* || die # Libs for file in "${S}"/lib/*; do if [[ -d ${file} ]]; then continue elif [[ -x ${file} ]]; then dolib.so ${file} || die else insinto /usr/$(get_libdir) doins ${file} || die fi done sed \ -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \ -i "${S}"/include/ccp4.setup-sh || die # Setup scripts insinto /etc/profile.d # newins "${S}"/include/ccp4.setup-bash ccp4.setup.bash || die newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die # newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die rm -f "${S}"/include/ccp4.setup* # Environment files, setup scripts, etc. insinto /usr/share/ccp4/include doins "${S}"/include/* || die # smartie -- log parsing insinto /usr/share/ccp4 doins -r "${S}"/share/smartie || die # Install docs and examples doman "${S}"/man/cat1/* mv "${S}"/manual/README "${S}"/manual/README-manual dodoc manual/* README CHANGES doc/* examples/README || die rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* rm "${ED}"/usr/share/doc/${PF}/COPYING.* dohtml -r "${S}"/html/* if use examples; then for i in data rnase toxd; do docinto examples/${i} dodoc "${S}"/examples/${i}/* done docinto examples/tutorial dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css for i in data results; do docinto examples/tutorial/${i} dodoc "${S}"/examples/tutorial/${i}/* done for i in non-runnable runnable; do docinto examples/unix/${i} dodoc "${S}"/examples/unix/${i}/* done fi # Needed for ccp4i docs to work dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die # Fix overlaps with other packages rm -f "${ED}"/usr/share/man/man1/rasmol.1* "${ED}"/usr/lib/font84.dat || die mv "${ED}"/usr/share/man/man1/truncate{,-ccp4}* || die cat >> "${T}"/baubles <<- EOF #!${EPREFIX}/bin/bash exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py EOF exeinto /usr/libexec/ccp4/bin/ doexe "${T}"/baubles || die } pkg_postinst() { einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" einfo "in ${EPREFIX}/etc/profile.d/ccp4.setup* to modify this." } # Epatch wrapper for bulk patching ccp_patch() { EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} }